The difference I know is that ffmpeg uses Lavf54.59.100 as Writing library and handbrake does libmkv 0.6.5 as Writing library.

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I found this problem in the summer of 2011. This problem arises and carries on in any input files, even now. The converted files can be playbacked with mplayer, mplayer2, ffplay, and vlc.

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The differences I find are that ffmpeg uses Lavf54.59.100 as Writing library and handbrake does libmkv 0.6.5 as Writing library, the displayed image size of ffmpeg is 854x480 and that of handbrake is 853x480.

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I don't convert to x264 files by multiAVCHD because multiAVCHD is windows app and convert speed is very very slow on emulation app of MacOSX.

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I couldn't have attached input and output files in this modification because of size limit 2.5 MB.